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BMRB: 19970

2MP8

NMR structure of NKR-5-3B

Authors

Rosengren, K., Craik, D.J.

Assembly

Enterocin NKR-5-3B

Entity

1. Enterocin NKR-5-3B (polymer, Thiol state: not present), 64 monomers, 6334.446 Da Detail

LTANLGISSY AAKKVIDIIN TGSAVATIIA LVTAVVGGGL ITAGIVATAK SLIKKYGAKY AAAW

Formula weight

6334.446 Da

Entity Connection

peptide 1 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	peptide	sing	1:LEU1:N	1:TRP64:C

Source organism

Enterococcus faecalis

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 69.8 %, Completeness (bb): 79.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	69.8 % (480 of 688)	76.0 % (259 of 341)	56.8 % (159 of 280)	92.5 % (62 of 67)
Backbone	79.9 % (307 of 384)	94.1 % (127 of 135)	64.9 % (120 of 185)	93.8 % (60 of 64)
Sidechain	62.6 % (226 of 361)	64.1 % (132 of 206)	60.5 % (92 of 152)	66.7 % (2 of 3)
Aromatic	5.6 % (2 of 36)	5.6 % (1 of 18)	5.9 % (1 of 17)	0.0 % (0 of 1)
Methyl	45.8 % (55 of 120)	45.0 % (27 of 60)	46.7 % (28 of 60)

1. NKR-5-3B

LTANLGISSY AAKKVIDIIN TGSAVATIIA LVTAVVGGGL ITAGIVATAK SLIKKYGAKY AAAW

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5

#	Name	Isotope labeling	Type	Concentration
1	NKR-5-3B	natural abundance		6 mg/mL
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 5

#	Name	Isotope labeling	Type	Concentration
4	NKR-5-3B	natural abundance		6 mg/mL
5	D2O	natural abundance		100 %

Protein Blocks Logo

Calculated from 20 models in PDB: 2MP8, Strand ID: A Detail

Release date

2015-05-10

Citation

Identification, Characterization, and Three-Dimensional Structure of the Novel Circular Bacteriocin, Enterocin NKR-5-3B, from Enterococcus faecium
Himeno, K., Rosengren, K., Inoue, T., Perez, R.H., Colgrave, M.L., Lee, H., Fujita, K., Ishibashi, N., Zendo, T., Wilaipun, P., Nakayama, J., Leelawatcharamas, V., Jikuya, H., Craik, D.J., Sonomoto, K.
Biochemistry (2015), 54, 4863-4876, PubMed 26174911 , DOI 10.1021/acs.biochem.5b00196 , Abstract

Related entities 1. Enterocin NKR-5-3B, : 1 : 15 entities Detail

Experiments performed 9 experiments Detail

1 2D DQF-COSY

Instrument

Bruker Avance - 600 MHz equipped with cryoprobe.

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5

#	Name	Isotope labeling	Type	Concentration
1	NKR-5-3B	natural abundance		6 mg/mL
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

2 2D 1H-1H TOCSY

Instrument

Bruker Avance - 600 MHz equipped with cryoprobe.

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5

#	Name	Isotope labeling	Type	Concentration
1	NKR-5-3B	natural abundance		6 mg/mL
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

3 2D 1H-1H NOESY

Instrument

Bruker Avance - 600 MHz equipped with cryoprobe.

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5

#	Name	Isotope labeling	Type	Concentration
1	NKR-5-3B	natural abundance		6 mg/mL
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

4 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz equipped with cryoprobe.

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5

#	Name	Isotope labeling	Type	Concentration
1	NKR-5-3B	natural abundance		6 mg/mL
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

5 2D 1H-1H TOCSY

Instrument

Bruker Avance - 600 MHz equipped with cryoprobe.

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 5

#	Name	Isotope labeling	Type	Concentration
4	NKR-5-3B	natural abundance		6 mg/mL
5	D2O	natural abundance		100 %

6 2D 1H-1H NOESY

Instrument

Bruker Avance - 600 MHz equipped with cryoprobe.

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 5

#	Name	Isotope labeling	Type	Concentration
4	NKR-5-3B	natural abundance		6 mg/mL
5	D2O	natural abundance		100 %

7 2D 1H-13C HSQC

Instrument

Bruker Avance - 600 MHz equipped with cryoprobe.

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 5

#	Name	Isotope labeling	Type	Concentration
4	NKR-5-3B	natural abundance		6 mg/mL
5	D2O	natural abundance		100 %

8 2D 1H-1H TOCSY

Instrument

Bruker Avance II - 900 MHz equipped with cryoprobe.

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5

#	Name	Isotope labeling	Type	Concentration
1	NKR-5-3B	natural abundance		6 mg/mL
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

9 2D 1H-1H NOESY

Instrument

Bruker Avance II - 900 MHz equipped with cryoprobe.

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5

#	Name	Isotope labeling	Type	Concentration
1	NKR-5-3B	natural abundance		6 mg/mL
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_19970_2mp8.nef
Input source #2: Coordindates	2mp8.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	True (see coordinates for details)
Overall data processing status	Warning

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

--------10--------20--------30--------40--------50--------60----
LTANLGISSYAAKKVIDIINTGSAVATIIALVTAVVGGGLITAGIVATAKSLIKKYGAKYAAAW
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LTANLGISSYAAKKVIDIINTGSAVATIIALVTAVVGGGLITAGIVATAKSLIKKYGAKYAAAW

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	64	0	0	100.0

Content subtype: combined_19970_2mp8.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	1		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	479		100.0 (chain: A, length: 64)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	1202 (1)	noe	100.0 (chain: A, length: 64)
2	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	93 (1)	hbond	92.2 (chain: A, length: 64)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	134 (134)	.	95.3 (chain: A, length: 64)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 64, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 263
  - ¹³C chemical shifts: 154
  - ¹⁵N chemical shifts: 62
- Completeness of assignments
  - Entity_assemble_ID: A
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_3
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 64, Sequence coverage: 100.0%
- Total number of restraints: 1202
- Weight of restraints: 1.0 (1202)
- Potential type of restraints: square-well-parabolic (1202)
- Range of distance target values: 1.16, 2.75 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_2
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 64, Sequence coverage: 92.2%
  - Total number of restraints: 93
  - Weight of restraints: 1.0 (93)
  - Potential type of restraints: square-well-parabolic (93)
  - Range of distance target values: 1.15, 1.65 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 64, Sequence coverage: 95.3%
- Total number of restraints: 134
- Total number of restraints per polymer type: 134
- Weight of restraints: 1.0 (134)
- Potential type of restraints: square-well-parabolic (134)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords antimicrobial peptide, bacteriocin, head-to-tail cyclic, helix bundle